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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ), 'gf_id' => 'HOM05D001155', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001155' ), 'data_identifier' => 'HOM05D001155', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001155', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A10p12280' => 'bna', 'A10p33720' => 'bna', 'Aa31LG10G9150' => 'aar', 'Aa31LG10G9160' => 'aar', 'Aa31LG1G22980' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3263' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2595' => 'aag', 'Actinidia05371' => 'ach', 'Actinidia23877' => 'ach', 'Ah.07g197170' => 'amhyb', 'Ah.09g233710' => 'amhyb', 'Ah.12g052290' => 'amhyb', 'AL6G10810' => 'aly', 'AL6G10820' => 'aly', 'AL7G18510' => 'aly', 'AL8G30430' => 'aly', 'Aqoxy1G03212' => 'aox', 'Aqoxy2G00261' => 'aox', 'Aqoxy4G02463' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1I7V20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54H2MY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5AIV52' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5NTT5I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.72KEI0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W099G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.914NIM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV1Y5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FXLQ18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9FEDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H76UH5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HS3YG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA5TJQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q4G2HA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN5QPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1M99V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWE764' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YWH2YP' => 'arhy', 'AT4G33070' => 'ath', 'AT5G01320' => 'ath', 'AT5G01330' => 'ath', 'AT5G54960' => 'ath', 'ATR0083G003' => 'atr', 'ATR0314G014' => 'atr', 'ATR0582G217' => 'atr', 'ATR0681G146' => 'atr', 'ATR0693G342' => 'atr', 'ATR0739G014' => 'atr', 'ATR0739G019' => 'atr', 'ATR0752G194' => 'atr', 'ATR0759G081' => 'atr', 'Atru.chr10.1707' => 'acertr', 'Atru.chr3.4170' => 'acertr', 'Atru.chr8.2279' => 'acertr', 'Atru.chr8.2280_Atru.chr8.2281' => 'acertr', 'AUR62010449' => 'cqu', 'AUR62030465' => 'cqu', 'AUR62031145' => 'cqu', 'AUR62036556' => 'cqu', 'BcaB05g21933' => 'bca', 'BcaB08g35862' => 'bca', 'BcaC03g13073' => 'bca', 'BcaC04g20284' => 'bca', 'BcaC06g31961' => 'bca', 'BcaC06g31974' => 'bca', 'BcaC06g31975' => 'bca', 'BcaC09g47999' => 'bca', 'BcaC09g48043' => 'bca', 'BNapus_Darmor_BZH_scaffold_167p00210' => 'bna', 'BolC1t05484H' => 'bol', 'BolC2t06020H' => 'bol', 'BolC9t57417H' => 'bol', 'BolC9t60196H' => 'bol', 'BraA01t04325Z' => 'bra', 'BraA02t04694Z' => 'bra', 'BraA10t43322Z' => 'bra', 'C02p00220' => 'bna', 'C09p45490' => 'bna', 'C09p74630' => 'bna', 'CAN.G1095.8' => 'can', 'CAN.G41.7' => 'can', 'CAN.G41.8' => 'can', 'CAN.G41.9' => 'can', 'CAN.G79.59' => 'can', 'CAN.G823.5' => 'can', 'CANSAT35G0704' => 'cansat', 'CANSAT35G1262' => 'cansat', 'CANSAT54G1173' => 'cansat', 'CARHR211690' => 'chi', 'CARHR241090' => 'chi', 'CARHR268300' => 'chi', 'Carub.0006s0049' => 'cru', 'Carub.0007s0738' => 'cru', 'Carub.0008s1525' => 'cru', 'Ca_00153_v3' => 'car', 'Ca_00154_v3' => 'car', 'Ca_00378_v3' => 'car', 'Ca_00421_v3' => 'car', 'Ca_06975_v3' => 'car', 'Ca_07665_v3' => 'car', 'Ca_20211_v3' => 'car', 'Ca_26748_v3' => 'car', 'Ca_30010_v3' => 'car', 'CBR_g18936' => 'cbr', 'CBR_g18938' => 'cbr', 'CBR_g18941' => 'cbr', 'CBR_g29370' => 'cbr', 'CBR_g29373' => 'cbr', 'Cc02_g14490' => 'ccan', 'Cc03_g06870' => 'ccan', 'Cc05_g02160' => 'ccan', 'Cc06_g01070' => 'ccan', 'CDE04G0138' => 'cde', 'CDE04G0334' => 'cde', 'CDE04G1146' => 'cde', 'CDE04G1508' => 'cde', 'CDE04G2180' => 'cde', 'CDE04G2488' => 'cde', 'CDE04G2965' => 'cde', 'CDE06G0433' => 'cde', 'CDE10G0147' => 'cde', 'CDE10G0869' => 'cde', 'Cfa000579' => 'cfa', 'Cfa000581' => 'cfa', 'Cfa011728' => 'cfa', 'Cfa017172' => 'cfa', 'Cfa022830' => 'cfa', 'Ciclev10011317m.g' => 'ccl', 'Ciclev10014703m.g' => 'ccl', 'CiPaw.09G211800' => 'cil', 'CiPaw.10G057400' => 'cil', 'CiPaw.10G118700' => 'cil', 'CiPaw.10G157900' => 'cil', 'CiPaw.10G158100' => 'cil', 'CiPaw.10G158200' => 'cil', 'CiPaw.14G057300' => 'cil', 'ClCG00G006170' => 'cla', 'ClCG01G023580' => 'cla', 'ClCG03G000570' => 'cla', 'ClCG04G006860' => 'cla', 'ClCG04G006870' => 'cla', 'ClCG04G006880' => 'cla', 'ClCG04G006890' => 'cla', 'ClCG10G022340' => 'cla', 'COL.COLO4_08002' => 'col', 'COL.COLO4_11094' => 'col', 'COL.COLO4_14501' => 'col', 'COL.COLO4_31335' => 'col', 'Cpa.g.sc120.23' => 'cpa', 'Cpa.g.sc120.49' => 'cpa', 'Cpa.g.sc7.43' => 'cpa', 'Cre03.g165700' => 'cre', 'CsaV3_1G036380' => 'csa', 'CsaV3_3G033550' => 'csa', 'CsaV3_4G026400' => 'csa', 'CsaV3_4G026410' => 'csa', 'CsaV3_4G026420' => 'csa', 'CsaV3_6G050730' => 'csa', 'CSS0001640' => 'camsi', 'CSS0004054' => 'camsi', 'CSS0004287' => 'camsi', 'CSS0009059' => 'camsi', 'CSS0012491' => 'camsi', 'CSS0013717' => 'camsi', 'CSS0014343' => 'camsi', 'CSS0016910' => 'camsi', 'CSS0019525' => 'camsi', 'CSS0022623' => 'camsi', 'CSS0028414' => 'camsi', 'CSS0033302' => 'camsi', 'CSS0035976' => 'camsi', 'CSS0037718' => 'camsi', 'CSS0042557' => 'camsi', 'DCAR_007969' => 'dca', 'DCAR_015387' => 'dca', 'DCAR_015388' => 'dca', 'DCAR_018682' => 'dca', 'DCAR_018949' => 'dca', 'Dinv01959' => 'din', 'Dinv04635' => 'din', 'Dinv09641' => 'din', 'Dinv13135' => 'din', 'Dinv13136' => 'din', 'Dinv18392' => 'din', 'Duzib093G1933' => 'dzi', 'Duzib128G0952' => 'dzi', 'Duzib168G1961' => 'dzi', 'Duzib192G0580' => 'dzi', 'Duzib235G0602' => 'dzi', 'ECA232G1976' => 'eca', 'ECA232G4863' => 'eca', 'ECA234G2505' => 'eca', 'ECA246G2066' => 'eca', 'ECA247G1587' => 'eca', 'ECA247G1617' => 'eca', 'ECA248G1750' => 'eca', 'EL10Ac5g12525' => 'bvu', 'EL10Ac8g20497' => 'bvu', 'Eucgr.A00546' => 'egr', 'Eucgr.A00547' => 'egr', 'Eucgr.A00548' => 'egr', 'Eucgr.A00549' => 'egr', 'Eucgr.D00535' => 'egr', 'Eucgr.D01319' => 'egr', 'Eucgr.J01896' => 'egr', 'Eucgr.K02968' => 'egr', 'Eucgr.K02969' => 'egr', 'Eucgr.L01136' => 'egr', 'Eucgr.L01137' => 'egr', 'Eucgr.L01139' => 'egr', 'Eucgr.L02239' => 'egr', 'Eucgr.L02272' => 'egr', 'FAN02G0686' => 'fan', 'FAN02G1182' => 'fan', 'FAN05G3257' => 'fan', 'FAN09G4812' => 'fan', 'FAN11G1082' => 'fan', 'FAN11G2788' => 'fan', 'FAN14G1251' => 'fan', 'FAN16G0567' => 'fan', 'FAN16G1685' => 'fan', 'FAN17G0173' => 'fan', 'FAN21G1534' => 'fan', 'FAN21G3818' => 'fan', 'FAN25G0551' => 'fan', 'FAN25G1133' => 'fan', 'FvH4_3g08040' => 'fve', 'FvH4_3g39060' => 'fve', 'FvH4_6g11100' => 'fve', 'Glyma.01G118000' => 'gma', 'Glyma.03G055100' => 'gma', 'Glyma.07G153100' => 'gma', 'Glyma.08G176600' => 'gma', 'Glyma.13G231700' => 'gma', 'Glyma.15G056400' => 'gma', 'Glyma.15G080800' => 'gma', 'Glyma.18G204200' => 'gma', 'Gohir.A05G156200' => 'ghi', 'Gohir.A08G000056' => 'ghi', 'Gohir.A09G166600' => 'ghi', 'Gohir.A09G166700' => 'ghi', 'Gohir.D05G159000' => 'ghi', 'Gohir.D08G008000' => 'ghi', 'Gohir.D09G162200' => 'ghi', 'Gohir.D09G162300' => 'ghi', 'Gohir.D10G031701' => 'ghi', 'Gorai.004G001200' => 'gra', 'Gorai.006G183900' => 'gra', 'Gorai.006G184000' => 'gra', 'Gorai.009G164100' => 'gra', 'Gorai.011G033400' => 'gra', 'GSVIVG01003940001' => 'vvi', 'GSVIVG01004503001' => 'vvi', 'GSVIVG01005052001' => 'vvi', 'GSVIVG01012373001' => 'vvi', 'GSVIVG01021184001' => 'vvi', 'GSVIVG01024702001' => 'vvi', 'HanXRQChr01g0005181' => 'han', 'HanXRQChr01g0016621' => 'han', 'HanXRQChr05g0152991' => 'han', 'HanXRQChr05g0154841' => 'han', 'HanXRQChr10g0293701' => 'han', 'HanXRQChr10g0293711' => 'han', 'HanXRQChr10g0293721' => 'han', 'HanXRQChr15g0464051' => 'han', 'HanXRQChr15g0490621' => 'han', 'HanXRQChr17g0555351' => 'han', 'Haze_06268' => 'cav', 'Haze_21032' => 'cav', 'Haze_24366' => 'cav', 'Hma1.2p1_0001F.1_g001790' => 'hma', 'Hma1.2p1_0362F.1_g136600' => 'hma', 'Hma1.2p1_1981F.1_g309910' => 'hma', 'HPP92_003700' => 'vpl', 'HPP92_012019' => 'vpl', 'HPP92_012028' => 'vpl', 'HPP92_012029' => 'vpl', 'HPP92_019011' => 'vpl', 'HPP92_019012' => 'vpl', 'HPP92_019096' => 'vpl', 'HPP92_019097' => 'vpl', 'Hund10969' => 'sun', 'Hund10971' => 'sun', 'Hund14891' => 'sun', 'Hund23877' => 'sun', 'Lalb_Chr01g0023181' => 'lal', 'Lalb_Chr07g0191401' => 'lal', 'Lalb_Chr18g0059191' => 'lal', 'Lalb_Chr19g0124361' => 'lal', 'Lj1g0005849' => 'lja', 'Lj2C1086T3' => 'lonja', 'Lj2C296G3' => 'lonja', 'Lj2C71T7' => 'lonja', 'Lj3g0023215' => 'lja', 'Lj6g0019898' => 'lja', 'Lj7C108T5' => 'lonja', 'Lsat_1_v5_gn_2_52200' => 'lsa', 'Lsat_1_v5_gn_2_52260' => 'lsa', 'Lsat_1_v5_gn_2_52280' => 'lsa', 'Lsat_1_v5_gn_2_52320' => 'lsa', 'Lsat_1_v5_gn_4_50121' => 'lsa', 'Lsat_1_v5_gn_4_50141' => 'lsa', 'Lsat_1_v5_gn_9_19100' => 'lsa', 'Lsat_1_v5_gn_9_34941' => 'lsa', 'Manes.08G094400' => 'mes', 'Manes.09G106300' => 'mes', 'Manes.14G086300' => 'mes', 'Manes.16G036400' => 'mes', 'Manes.17G053600' => 'mes', 'Mapoly0095s0010' => 'mpo', 'Mapoly0160s0004' => 'mpo', 'MBI05_g35511_MAGBIO' => 'mbi', 'MBI05_g39186_MAGBIO' => 'mbi', 'MBI07_g17048_MAGBIO' => 'mbi', 'MBI08_g23272_MAGBIO' => 'mbi', 'MBI15_g23051_MAGBIO' => 'mbi', 'MBI16_g04465_MAGBIO' => 'mbi', 'MD00G1062400' => 'mdo', 'MD03G1065100' => 'mdo', 'MD04G1159900' => 'mdo', 'MD04G1160100' => 'mdo', 'MD07G1137600' => 'mdo', 'MD10G1283500' => 'mdo', 'MD11G1069100' => 'mdo', 'MD12G1172400' => 'mdo', 'MD12G1172500' => 'mdo', 'MD12G1173200' => 'mdo', 'Medtr1g011530' => 'mtr', 'Medtr2g009330' => 'mtr', 'Medtr2g015560' => 'mtr', 'Medtr4g017200' => 'mtr', 'Medtr5g046610' => 'mtr', 'Medtr5g046620' => 'mtr', 'Medtr7g069500' => 'mtr', 'Medtr7g069540' => 'mtr', 'MELO3C007227.2' => 'cme', 'MELO3C009145.2' => 'cme', 'MELO3C020531.2' => 'cme', 'MELO3C026004.2' => 'cme', 'MELO3C026005.2' => 'cme', 'MELO3C026007.2' => 'cme', 'Migut.I00033' => 'egut', 'Migut.J00132' => 'egut', 'Migut.M01059' => 'egut', 'Migut.M01062' => 'egut', 'MSTRG.18992' => 'ama', 'MSTRG.23110' => 'ama', 'MSTRG.26823' => 'ama', 'MSTRG.5561' => 'ama', 'MSTRG.7390' => 'ama', 'Nitab4.5_0000195g0220' => 'nta', 'Nitab4.5_0000376g0160' => 'nta', 'Nitab4.5_0000444g0150' => 'nta', 'Nitab4.5_0000839g0110' => 'nta', 'Nitab4.5_0001645g0050' => 'nta', 'Nitab4.5_0003514g0040' => 'nta', 'Nitab4.5_0012964g0010' => 'nta', 'Nitab4.5_0013789g0010' => 'nta', 'Nn1g04355' => 'nnu', 'Nn1g09049' => 'nnu', 'Nn2g10917' => 'nnu', 'Nn2g10919' => 'nnu', 'Nn2g10921' => 'nnu', 'Nn2g10922' => 'nnu', 'Nn2g10935' => 'nnu', 'Nn2g13185' => 'nnu', 'Oeu020592.1' => 'oeu', 'Oeu033575.1' => 'oeu', 'Oeu041562.1' => 'oeu', 'Oeu063392.1' => 'oeu', 'Os01g0160100' => 'osa', 'Os03g0293500' => 'osa', 'Os05g0469600' => 'osa', 'Os05g0469800' => 'osa', 'Os07g0693100' => 'osa', 'Os10g0480900' => 'osa', 'Peaxi162Scf00014g00030' => 'pax', 'Peaxi162Scf00540g10015' => 'pax', 'Peaxi162Scf00620g00003' => 'pax', 'Peaxi162Scf01132g00137' => 'pax', 'Peaxi162Scf01132g00138' => 'pax', 'PGR004G0683' => 'pgr', 'PGR004G2870' => 'pgr', 'PGR031G0864' => 'pgr', 'PGR119G1036' => 'pgr', 'PGSC0003DMG400006270' => 'stu', 'PGSC0003DMG400022953' => 'stu', 'PGSC0003DMG400030369' => 'stu', 'PGSC0003DMG400038451' => 'stu', 'Phvul.006G177600' => 'pvu', 'Phvul.008G095400' => 'pvu', 'Phvul.010G078000' => 'pvu', 'Potri.004G054100' => 'ptr', 'Potri.006G102500' => 'ptr', 'Potri.011G064000' => 'ptr', 'Potri.016G120100' => 'ptr', 'Potri.017G151900' => 'ptr', 'Pp3c17_2040' => 'ppa', 'Pp3c19_19330' => 'ppa', 'Pp3c1_22470' => 'ppa', 'Pp3c3_12170' => 'ppa', 'Pp3c3_15510' => 'ppa', 'Prupe.1G078900' => 'ppe', 'Prupe.4G058300' => 'ppe', 'Prupe.6G054000' => 'ppe', 'Prupe.6G280700' => 'ppe', 'Prupe.6G280800' => 'ppe', 'Psat0s3493g0080' => 'psa', 'Psat0s3493g0120' => 'psa', 'Psat1g199560' => 'psa', 'Psat3g125480' => 'psa', 'Psat3g125520' => 'psa', 'PSO135G0039' => 'pso', 'PSO170G3880' => 'pso', 'PSO339G5230' => 'pso', 'PSO384G0801' => 'pso', 'PSO478G0293' => 'pso', 'PSO478G5193' => 'pso', 'PSO541G1580' => 'pso', 'PSO675G5973' => 'pso', 'PSO761G0681' => 'pso', 'PSO782G1598' => 'pso', 'QL05p044885' => 'qlo', 'QL07p034707' => 'qlo', 'QL07p034831' => 'qlo', 'QL07p034843' => 'qlo', 'QL08p015811' => 'qlo', 'QL08p015874' => 'qlo', 'RcHm_v2.0_Chr3g0462531' => 'rch', 'RcHm_v2.0_Chr5g0010191' => 'rch', 'RcHm_v2.0_Chr5g0010251' => 'rch', 'RcHm_v2.0_Chr5g0070371' => 'rch', 'RcHm_v2.0_Chr7g0223061' => 'rch', 'Rhsim01G0238800' => 'rsi', 'Rhsim02G0073300' => 'rsi', 'Rhsim03G0041200' => 'rsi', 'Rhsim05G0073100' => 'rsi', 'Rhsim05G0219500' => 'rsi', 'Rhsim05G0219700' => 'rsi', 'Rhsim06G0129500' => 'rsi', 'Rhsim06G0200000' => 'rsi', 'Rhsim12G0097300' => 'rsi', 'Rhsim12G0145900' => 'rsi', 'Rhsim13G0186600' => 'rsi', 'RhsimUnG0075600' => 'rsi', 'Sabra04G0035500' => 'sbr', 'Sabra06G0078600' => 'sbr', 'Sabra06G0078800' => 'sbr', 'Sabra11G0045700' => 'sbr', 'Sabra16G0116000' => 'sbr', 'SalBow4G0631' => 'sbo', 'SalBow4G2813' => 'sbo', 'SalBow5G1913' => 'sbo', 'SalBow5G2009' => 'sbo', 'SalBow5G3011' => 'sbo', 'SalBow8G3940' => 'sbo', 'Sc22g0002580' => 'sci', 'Sed0003232' => 'sed', 'Sed0010433' => 'sed', 'Sed0013145' => 'sed', 'Sed0013224' => 'sed', 'SEGI_02739' => 'sgi', 'SEGI_22273' => 'sgi', 'SEGI_32038' => 'sgi', 'SGA_v2.0_scaffold16G07668' => 'sas', 'SGA_v2.0_scaffold22G09666' => 'sas', 'SGA_v2.0_scaffold245G44643' => 'sas', 'SGA_v2.0_scaffold85G26716' => 'sas', 'SGA_v2.0_scaffold90G27961' => 'sas', 'SGA_v2.0_scaffold90G27963' => 'sas', 'SGA_v2.0_scaffold90G27971' => 'sas', 'SGA_v2.0_scaffold90G27974' => 'sas', 'SHI12856' => 'shi', 'SMO171G0043' => 'smo', 'SMO307G0016' => 'smo', 'SMO334G0089' => 'smo', 'SMO353G0250' => 'smo', 'SMO358G0172' => 'smo', 'Solyc06g082130.3' => 'sly', 'Solyc09g005110.3' => 'sly', 'Solyc10g076510.2' => 'sly', 'Sopen02g022160' => 'spe', 'Sopen06g033520' => 'spe', 'Sopen09g001090' => 'spe', 'Sopen10g028150' => 'spe', 'Sp3g07400' => 'spa', 'Sp6g16910' => 'spa', 'Sp6g40640' => 'spa', 'TAR369G0729' => 'tar', 'TAR438G0001' => 'tar', 'TAR580G0001' => 'tar', 'TAR623G1032' => 'tar', 'TAR624G0888' => 'tar', 'TAR629G2594' => 'tar', 'TAR633G2773' => 'tar', 'THA.LOC104805986' => 'tha', 'THA.LOC104816205' => 'tha', 'THA.LOC104823375' => 'tha', 'THA.LOC104827046' => 'tha', 'Thecc.05G011600' => 'tca', 'Thecc.05G011700' => 'tca', 'Thecc.05G011900' => 'tca', 'Thecc.05G012000' => 'tca', 'Thecc.06G174400' => 'tca', 'Thecc.09G351900' => 'tca', 'Thhalv10013008m.g' => 'esa', 'Thhalv10013010m.g' => 'esa', 'TPR.G11783' => 'tpr', 'TPR.G14290' => 'tpr', 'TPR.G18378' => 'tpr', 'TPR.G29445' => 'tpr', 'TPR.G34798' => 'tpr', 'TPR.G35442' => 'tpr', 'TPR.G35450' => 'tpr', 'TPR.G9481' => 'tpr', 'TWI74G0509' => 'twi', 'TWI75G0434' => 'twi', 'TWI77G0640' => 'twi', 'vmacro03879' => 'vma', 'vmacro03880' => 'vma', 'vmacro08894' => 'vma', 'vmacro13187' => 'vma', 'vmacro14610' => 'vma', 'vmacro19580' => 'vma', 'vmacro20301' => 'vma', 'VMungo0331G1187' => 'vmu', 'VMungo0540G0630' => 'vmu', 'VMungo0540G2520' => 'vmu', 'VMungo1383G0386' => 'vmu', 'Zm00001eb013520' => 'zma', 'Zm00001eb082440' => 'zma', 'Zm00001eb303340' => 'zma', 'Zm00001eb331530' => 'zma', 'Zm00001eb336190' => 'zma', 'Zm00001eb351810' => 'zma', 'Zm00001eb421320' => 'zma' ) $gf_id = 'HOM05D001155' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001155' ) $data_identifier = 'HOM05D001155' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 9, 'cbr' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 5, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 8, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 15, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 6, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 8, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 12, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 1, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 6, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421320' $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